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Reaction frames were then constructed using these duplicated and renamed compound frames.
Finally, the isoforms were associated with reaction frames constructed from the renamed compound frames.
The cytosolic reaction frame was created using the compound frames CY_UDP-D-glucuronate and CY_UDP-D-xylose and the compound frames GL_UDP-D-glucuronate and GL_UDP-D-xylose were used to populate the Golgi reaction frame.
The current scheme presents some challenges a formal schema that included compartmentalization information in compound frames would surmount.
Existing compound frames were duplicated and assigned names containing two-letter prefixes, which have been enumerated in Table 3.
The current Pathway Tools distribution allows the association of Cellular Component Gene Ontology terms with protein frames only and not with the compound frames for metabolites.
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A generic nonlinear compound frame model is developed and applied for investigation of arching action in reinforced concrete beams.
Naturally, more detailed encoding of the sub-cellular localization in the compound frame names could be achieved simply through expansion of the lexicon in Table 3 our chosen degree of granularity simply reflected the limited extent of our present knowledge.
Second, translation of a PGDB to a future version with an explicit localization slot in any compound frame should be fairly trivial, by collapsing the multiple prefixed identifiers for a given compound back to a single frame with a 'compartment' slot filled in with the appropriate term.
Table 2 Elemental composition of the two potential OBPs identified by the differential analysis software compared to that of the parent compound E1 Frame number m/z Elemental composition RDBE Δ mmu (E1) 269.155317.14008O2 8.5 0.667 9 275.12930 C18H21O5 7.5 0.633 78 317.14008 C11H25O108.5 0.633 C11H25O10 −0.5 −5.240 RDBE: Ring and double bond equivalents.
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